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Clayton EW, Bland HT, Mittendorf KF. Protecting Privacy of Pregnant and LGBTQ+ Research Participants. JAMA 2024:2817544. [PMID: 38619831 DOI: 10.1001/jama.2024.4837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
This Viewpoint summarizes existing federal regulations aimed at protecting research data, describes the challenges of enforcing these regulations, and discusses how evolving privacy technologies could be used to reduce health disparities and advance health equity among pregnant and LGBTQ+ research participants.
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Affiliation(s)
- Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center and Vanderbilt University, Nashville, Tennessee
| | - Harris T Bland
- Vanderbilt University Medical Center, Nashville, Tennessee
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Groom HC, Brooks NB, Weintraub ES, Slaughter MT, Mittendorf KF, Naleway AL. Incidence of Adolescent Syncope and Related Injuries Following Vaccination and Routine Venipuncture. J Adolesc Health 2024; 74:696-702. [PMID: 38069938 PMCID: PMC10960660 DOI: 10.1016/j.jadohealth.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/25/2023] [Accepted: 11/01/2023] [Indexed: 03/24/2024]
Abstract
PURPOSE Vaccination is associated with syncope in adolescents. However, incidence of vaccine-associated syncope and resulting injury, and how it compares to syncope incidence following other medical procedures, is not known. Here, we describe the incidence of syncope and syncope-related injury in adolescents following vaccination and routine venipuncture. METHODS We identified all Kaiser Permanente Northwest members ages 9-18 years with a vaccination or routine venipuncture and a same-day International Classification of Diseases diagnosis of syncope from 2013 through 2019. All cases were chart reviewed to establish chronology of events (vaccination, venipuncture, syncope, and injury, as applicable) and to attribute cause to vaccination or venipuncture. Incidence rates for vaccine-associated and venipuncture-associated syncope were calculated overall, by sex and age group. Syncope events resulting in injury were assessed for each event type. RESULTS Of 197,642 vaccination and 12,246 venipuncture events identified, 549 vaccination and 67 venipuncture events had same-day syncope codes. Chart validation confirmed 59/549 (10.7%) events as vaccine-associated syncope, for a rate of 2.99 per 10,000 vaccination events (95% confidence interval (CI): 2.27-3.85) and 20/67 (29.9%) events as venipuncture-associated syncope, for a rate of 16.33 per 10,000 venipuncture events (95% CI: 9.98-25.21). The incidence rate ratio of vaccine-associated to venipuncture-associated syncope events was 0.18 (95% CI: 0.11-0.31). The incidence of vaccine-associated syncope increased with each additional simultaneously administered vaccine, from 1.51 per 10,000 vaccination events (95% CI: 0.93-2.30) following a single vaccine to 9.94 per 10,000 vaccination events (95% CI: 6.43-14.67) following three or more vaccines. Syncope resulted in injury in about 15% of both vaccine and venipuncture events. DISCUSSION Syncope occurs more commonly following venipuncture than vaccination. The number of simultaneously administered vaccines is a risk factor for postvaccination syncope in adolescents.
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Affiliation(s)
- Holly C Groom
- Kaiser Permanente Center for Health Research, Portland, Oregon.
| | - Neon B Brooks
- Kaiser Permanente Center for Health Research, Portland, Oregon
| | - Eric S Weintraub
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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3
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Lippenszky L, Mittendorf KF, Kiss Z, LeNoue-Newton ML, Napan-Molina P, Rahman P, Ye C, Laczi B, Csernai E, Jain NM, Holt ME, Maxwell CN, Ball M, Ma Y, Mitchell MB, Johnson DB, Smith DS, Park BH, Micheel CM, Fabbri D, Wolber J, Osterman TJ. Prediction of Effectiveness and Toxicities of Immune Checkpoint Inhibitors Using Real-World Patient Data. JCO Clin Cancer Inform 2024; 8:e2300207. [PMID: 38427922 PMCID: PMC10919473 DOI: 10.1200/cci.23.00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/15/2023] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
PURPOSE Although immune checkpoint inhibitors (ICIs) have improved outcomes in certain patients with cancer, they can also cause life-threatening immunotoxicities. Predicting immunotoxicity risks alongside response could provide a personalized risk-benefit profile, inform therapeutic decision making, and improve clinical trial cohort selection. We aimed to build a machine learning (ML) framework using routine electronic health record (EHR) data to predict hepatitis, colitis, pneumonitis, and 1-year overall survival. METHODS Real-world EHR data of more than 2,200 patients treated with ICI through December 31, 2018, were used to develop predictive models. Using a prediction time point of ICI initiation, a 1-year prediction time window was applied to create binary labels for the four outcomes for each patient. Feature engineering involved aggregating laboratory measurements over appropriate time windows (60-365 days). Patients were randomly partitioned into training (80%) and test (20%) sets. Random forest classifiers were developed using a rigorous model development framework. RESULTS The patient cohort had a median age of 63 years and was 61.8% male. Patients predominantly had melanoma (37.8%), lung cancer (27.3%), or genitourinary cancer (16.4%). They were treated with PD-1 (60.4%), PD-L1 (9.0%), and CTLA-4 (19.7%) ICIs. Our models demonstrate reasonably strong performance, with AUCs of 0.739, 0.729, 0.755, and 0.752 for the pneumonitis, hepatitis, colitis, and 1-year overall survival models, respectively. Each model relies on an outcome-specific feature set, though some features are shared among models. CONCLUSION To our knowledge, this is the first ML solution that assesses individual ICI risk-benefit profiles based predominantly on routine structured EHR data. As such, use of our ML solution will not require additional data collection or documentation in the clinic.
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Affiliation(s)
- Levente Lippenszky
- Science and Technology Organization—Artificial Intelligence & Machine Learning, GE HealthCare, Budapest, Hungary/San Ramon, CA
| | | | - Zoltán Kiss
- Science and Technology Organization—Artificial Intelligence & Machine Learning, GE HealthCare, Budapest, Hungary/San Ramon, CA
| | - Michele L. LeNoue-Newton
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Pablo Napan-Molina
- Science and Technology Organization—Artificial Intelligence & Machine Learning, GE HealthCare, Budapest, Hungary/San Ramon, CA
| | - Protiva Rahman
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
- Health Outcomes and Biomedical Informatics, University of Florida, Tallahassee, FL
| | - Cheng Ye
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Balázs Laczi
- Science and Technology Organization—Artificial Intelligence & Machine Learning, GE HealthCare, Budapest, Hungary/San Ramon, CA
| | - Eszter Csernai
- Science and Technology Organization—Artificial Intelligence & Machine Learning, GE HealthCare, Budapest, Hungary/San Ramon, CA
| | - Neha M. Jain
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- OneOncology, Nashville, TN
| | - Marilyn E. Holt
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Sarah Cannon Research Institute, Nashville, TN
| | - Christina N. Maxwell
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Madeleine Ball
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Yufang Ma
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Department of Pharmaceutical Services, Vanderbilt University Medical Center, Nashville, TN
| | - Margaret B. Mitchell
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA
| | - Douglas B. Johnson
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - David S. Smith
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Ben H. Park
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Christine M. Micheel
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Daniel Fabbri
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Jan Wolber
- Pharmaceutical Diagnostics, GE HealthCare, Chalfont St Giles, United Kingdom
| | - Travis J. Osterman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
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Casillan A, Florido ME, Galarza-Cornejo J, Bakken S, Lynch JA, Chung WK, Mittendorf KF, Berner ES, Connolly JJ, Weng C, Holm IA, Khan A, Kiryluk K, Limdi NA, Petukhova L, Sabatello M, Wynn J. Participant-guided development of bilingual genomic educational infographics for Electronic Medical Records and Genomics Phase IV study. J Am Med Inform Assoc 2024; 31:306-316. [PMID: 37860921 PMCID: PMC10797276 DOI: 10.1093/jamia/ocad207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
OBJECTIVE Developing targeted, culturally competent educational materials is critical for participant understanding of engagement in a large genomic study that uses computational pipelines to produce genome-informed risk assessments. MATERIALS AND METHODS Guided by the Smerecnik framework that theorizes understanding of multifactorial genetic disease through 3 knowledge types, we developed English and Spanish infographics for individuals enrolled in the Electronic Medical Records and Genomics Network. Infographics were developed to explain concepts in lay language and visualizations. We conducted iterative sessions using a modified "think-aloud" process with 10 participants (6 English, 4 Spanish-speaking) to explore comprehension of and attitudes towards the infographics. RESULTS We found that all but one participant had "awareness knowledge" of genetic disease risk factors upon viewing the infographics. Many participants had difficulty with "how-to" knowledge of applying genetic risk factors to specific monogenic and polygenic risks. Participant attitudes towards the iteratively-refined infographics indicated that design saturation was reached. DISCUSSION There were several elements that contributed to the participants' comprehension (or misunderstanding) of the infographics. Visualization and iconography techniques best resonated with those who could draw on prior experiences or knowledge and were absent in those without. Limited graphicacy interfered with the understanding of absolute and relative risks when presented in graph format. Notably, narrative and storytelling theory that informed the creation of a vignette infographic was most accessible to all participants. CONCLUSION Engagement with the intended audience who can identify strengths and points for improvement of the intervention is necessary to the development of effective infographics.
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Affiliation(s)
- Aimiel Casillan
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, United States
| | - Jamie Galarza-Cornejo
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Suzanne Bakken
- Department of Nursing Scholarship and Research, School of Nursing, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - John A Lynch
- Department of Communication, School of Communication, Film, and Media Studies, University of Cincinnati, Cincinnati, OH 45221, United States
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Eta S Berner
- Department of Health Services Administration, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - John J Connolly
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, United States
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, United States
| | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, United States
| | - Lynn Petukhova
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, NY 10032, United States
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Maya Sabatello
- Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Medical Humanities and Ethics, Division of Ethics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Julia Wynn
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
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5
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Gilmore MJ, Knerr S, Kraft SA, Bulkley JE, Biesecker BB, Feigelson HS, Hunter JE, Jenkins CL, Kauffman TL, Lee SSJ, Liles EG, Mittendorf KF, Muessig KR, Porter KM, Rolf BA, Rope AF, Zepp JM, Anderson KP, Devine B, Joseph G, Leo MC, Goddard K, Wilfond BS. Improving Care for Marginalized Populations at Risk for Hereditary Cancer Syndromes: Innovations that Expanded Reach in the CHARM Study. Public Health Genomics 2023; 27:16-22. [PMID: 38142673 DOI: 10.1159/000535610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Affiliation(s)
- Marian J Gilmore
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA,
| | - Sarah Knerr
- Department of Health Systems and Population Health, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics and Palliative Care, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | | | | | - Jessica Ezzell Hunter
- Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA
| | - Charisma L Jenkins
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Tia L Kauffman
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, New York, USA
| | | | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Kristin R Muessig
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics and Palliative Care, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Bradley A Rolf
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, Washington, USA
| | - Alan F Rope
- Genome Medical, South San Francisco, California, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | | | - Beth Devine
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, California, USA
| | - Michael C Leo
- Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Katrina Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics and Palliative Care, Seattle Children's Research Institute, Seattle, Washington, USA
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6
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Knerr S, Guo B, Wernli KJ, Mittendorf KF, Feigelson HS, Gilmore MJ, Jarvik GP, Kauffman TL, Keast E, Liles EG, Lynch FL, Muessig KR, Okuyama S, Veenstra DL, Zepp JM, Wilfond BS, Devine B, Goddard KAB. Longitudinal adherence to breast cancer surveillance following cancer genetic testing in an integrated health care system. Breast Cancer Res Treat 2023; 201:461-470. [PMID: 37470892 PMCID: PMC10503958 DOI: 10.1007/s10549-023-07007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023]
Abstract
PURPOSE Screening with mammography and breast magnetic resonance imaging (MRI) is an important risk management strategy for individuals with inherited pathogenic variants (PVs) in genes associated with increased breast cancer risk. We describe longitudinal screening adherence in individuals who underwent cancer genetic testing as part of usual care in a vertically integrated health system. METHODS We determined the proportion time covered (PTC) by annual mammography and breast MRI for individuals with PVs in TP53, BRCA1, BRCA2, PALB2, NF1, CHEK2, and ATM. We determined time covered by biennial mammography beginning at age 50 years for individuals who received negative results, uncertain results, or with PVs in genes without specific breast cancer screening recommendations. RESULTS One hundred and forty individuals had PVs in TP53, BRCA1, BRCA2, PALB2, NF1, CHEK2, or ATM. Among these individuals, average PTC was 48% (range 0-99%) for annual screening mammography and 34% (range 0-100%) for annual breast MRI. Average PTC was highest for individuals with PVs in CHEK2 (N = 14) and lowest for individuals with PVs in TP53 (N = 3). Average PTC for biennial mammography (N = 1,027) was 49% (0-100%). CONCLUSION Longitudinal screening adherence in individuals with PVs in breast cancer associated genes, as measured by the proportion of time covered, is low; adherence to annual breast MRI falls below that of annual mammography. Additional research should examine screening behavior in individuals with PVs in breast cancer associated genes with a goal of developing interventions to improve adherence to recommended risk management.
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Affiliation(s)
- Sarah Knerr
- Department of Health Systems and Population Health, School of Public Health, University of Washington, Box 351621, Seattle, WA, 98195, USA.
| | - Boya Guo
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Karen J Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Marian J Gilmore
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Gail P Jarvik
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Tia L Kauffman
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Erin Keast
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | | | - Frances L Lynch
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Kristin R Muessig
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Sonia Okuyama
- Denver Health and Hospital Authority, Denver, CO, USA
| | - David L Veenstra
- Department of Pharmacy, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Benjamin S Wilfond
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Beth Devine
- Department of Health Systems and Population Health, School of Public Health, University of Washington, Box 351621, Seattle, WA, 98195, USA
- Department of Pharmacy, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
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7
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Bland HT, Gilmore MJ, Andujar J, Martin MA, Celaya-Cobbs N, Edwards C, Gerhart M, Hooker GW, Kraft SA, Marshall DR, Orlando LA, Paul NA, Pratap S, Rosenbloom ST, Wiesner GL, Mittendorf KF. Conducting inclusive research in genetics for transgender, gender-diverse, and sex-diverse individuals: Case analyses and recommendations from a clinical genomics study. J Genet Couns 2023:10.1002/jgc4.1785. [PMID: 37667436 PMCID: PMC10909936 DOI: 10.1002/jgc4.1785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/26/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
A person's phenotypic sex (i.e., endogenous expression of primary, secondary, and endocrinological sex characteristics) can impact crucial aspects of genetic assessment and resulting clinical care recommendations. In studies with genetics components, it is critical to collect phenotypic sex, information about current organ/tissue inventory and hormonal milieu, and gender identity. If researchers do not carefully construct data models, transgender, gender diverse, and sex diverse (TGSD) individuals may be given inappropriate care recommendations and/or be subjected to misgendering, inflicting medical and psychosocial harms. The recognized need for an inclusive care experience should not be limited to clinical practice but should extend to the research setting, where researchers must build an inclusive experience for TGSD participants. Here, we review three TGSD participants in the Family History and Cancer Risk Study (FOREST) to critically evaluate sex- and gender-related survey measures and associated data models in a study seeking to identify patients at risk for hereditary cancer syndromes. Furthermore, we leverage these participants' responses to sex- and gender identity-related questions in FOREST to inform needed changes to the FOREST data model and to make recommendations for TGSD-inclusive genetics research design, data models, and processes.
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Affiliation(s)
- Harris T. Bland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Marian J. Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Justin Andujar
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Makenna A. Martin
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Natasha Celaya-Cobbs
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Clasherrol Edwards
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville TN
| | - Meredith Gerhart
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Gillian W. Hooker
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
- Concert Genetics, Nashville TN
| | - Stephanie A. Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Research Institute, Seattle, WA 98101
- Department of Pediatrics, Bioethics and Palliative Care, University of Washington School of Medicine, Seattle, WA
| | - Dana R. Marshall
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College, Nashville TN
| | - Lori A. Orlando
- Duke University, Center for Applied Genomics and Precision Medicine, Durham, NC
| | - Natalie A. Paul
- Rainbow Advocacy Inclusion and Networking Services, Longview, WA
- Lavender Spectrum Health, Vancouver, WA
| | - Siddharth Pratap
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville TN
| | - S. Trent Rosenbloom
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Georgia L. Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
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8
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Guo B, Knerr S, Kauffman TL, Mittendorf KF, Keast E, Gilmore MJ, Feigelson HS, Lynch FL, Muessig KR, Okuyama S, Zepp JM, Veenstra DL, Hsu L, Phipps AI, Lindström S, Leo MC, Goddard KAB, Wilfond BS, Devine B. Risk management actions following genetic testing in the Cancer Health Assessments Reaching Many (CHARM) Study: A prospective cohort study. Cancer Med 2023; 12:19112-19125. [PMID: 37644850 PMCID: PMC10557878 DOI: 10.1002/cam4.6485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Genetic testing can identify cancer risk early, enabling prevention and early detection. We describe use of risk management interventions following genetic testing in the Cancer Health Assessment Reaching Many (CHARM) study. CHARM assessed risk and provided genetic testing to low income, low literacy, and other underserved populations that historically face barriers to accessing cancer genetic services. METHODS CHARM was implemented in Kaiser Permanente Northwest (KPNW) and Denver Health (DH) between 2018 and 2020. We identified post-testing screening (mammography, breast MRI, colonoscopy) and surgical (mastectomy, oophorectomy) procedures using electronic health records. We examined utilization in participants who did and did not receive actionable risk management recommendations from study genetic counselors following national guidelines. RESULTS CHARM participants were followed for an average of 15.4 months (range: 0.4-27.8 months) after results disclosure. Less than 2% (11/680) received actionable risk management recommendations (i.e., could be completed in the initial years following testing) based on their test result. Among those who received actionable recommendations, risk management utilization was moderate (54.5%, 6/11 completed any procedure) and varied by procedure (mammogram: 0/3; MRI: 2/4; colonoscopy: 4/5; mastectomy: 1/5; oophorectomy: 0/3). Cancer screening and surgery procedures were rare in participants without actionable recommendations. CONCLUSION Though the number of participants who received actionable risk management recommendations was small, our results suggest that implementing CHARM's risk assessment and testing model increased access to evidence-based genetic services and provided opportunities for patients to engage in recommended preventive care, without encouraging risk management overuse.
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Affiliation(s)
- Boya Guo
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Sarah Knerr
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Kathleen F. Mittendorf
- Vanderbilt‐Ingram Cancer CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Erin Keast
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Marian J. Gilmore
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | | | - Frances L. Lynch
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Kristin R. Muessig
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - Sonia Okuyama
- Division of Oncology, Denver Health and Hospital AuthorityDenverColoradoUSA
| | - Jamilyn M. Zepp
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - David L. Veenstra
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
| | - Li Hsu
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Amanda I. Phipps
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Sara Lindström
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Michael C. Leo
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Katrina A. B. Goddard
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - Benjamin S. Wilfond
- Treuman Katz Center for Pediatric BioethicsSeattle Children's Research InstituteSeattleWashingtonUSA
- Department of Pediatrics, Division of Bioethics and Palliative CareUniversity of WashingtonSeattleWashingtonUSA
| | - Beth Devine
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
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9
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Song J, Forrest N, Gordon A, Kottyan L, Mittendorf KF, Wei WQ, Ramsey-Goldman R, Walunas T, Kho A. Utilization of electronic health record data to evaluate the association of urban environment with systemic lupus erythematosus symptoms. Rheumatology (Oxford) 2023; 62:e180-e181. [PMID: 36383166 PMCID: PMC10234196 DOI: 10.1093/rheumatology/keac647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Janet Song
- Center for Health Information Partnerships, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Division of General Internal Medicine and Geriatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Noah Forrest
- Center for Health Information Partnerships, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Division of General Internal Medicine and Geriatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam Gordon
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Theresa Walunas
- Center for Health Information Partnerships, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Division of General Internal Medicine and Geriatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Abel Kho
- Center for Health Information Partnerships, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Division of General Internal Medicine and Geriatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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10
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Naleway AL, Henninger ML, Irving SA, Bianca Salas S, Kauffman TL, Crane B, Mittendorf KF, Harsh S, Elder C, Gee J. Epidemiology of Upper Limb Complex Regional Pain Syndrome in a Retrospective Cohort of Persons Aged 9-30 Years, 2002-2017. Perm J 2023:1-12. [PMID: 37154719 DOI: 10.7812/tpp/22.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Introduction This paper describes the epidemiology and clinical presentation of complex regional pain syndrome (CRPS) in a large, integrated health care delivery system; and CRPS incidence rates (IRs) over a time period spanning human papillomavirus (HPV) vaccine licensure and published case reports of CRPS following HPV vaccination. Methods The authors examined CRPS diagnoses in patients aged 9-30 years between January 2002 and December 2017 using electronic medical records, excluding patients with lower limb diagnoses only. Medical record abstraction and adjudication were conducted to verify diagnoses and describe clinical characteristics. CRPS IRs were calculated for 3 periods: Period 1 (2002-2006: before HPV vaccine licensure), Period 2 (2007-2012: after licensure but before published case reports), and Period 3 (2013-2017: after published case reports). Results A total of 231 individuals received an upper limb or unspecified CRPS diagnosis code during the study period; 113 cases were verified through abstraction and adjudication. Most verified cases (73%) were associated with a clear precipitating event (eg, non-vaccine-related injury, surgical procedure). The authors identified only 1 case in which a practitioner attributed CRPS onset to HPV vaccination. Twenty-five incident cases occurred in Period 1 (IR = 4.35/100,000 person-years (PY), 95% confidence interval (CI) = 2.94-6.44), 42 in Period 2 (IR = 5.94/100,000 PY, 95% CI = 4.39-8.04), and 29 in Period 3 (IR = 4.53/100,000 PY, 95% CI = 3.15-6.52); differences between periods were not statistically significant. Conclusion These data provide a comprehensive assessment of the epidemiology and characteristics of CRPS in children and young adults and provide further reassurance about the safety of HPV vaccination.
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Affiliation(s)
| | | | | | - S Bianca Salas
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Tia L Kauffman
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Bradley Crane
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stacy Harsh
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Charles Elder
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Julianne Gee
- Immunization Safety Office, Centers for Disease Control and Prevention, Atlanta, GA, USA
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11
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Okuyama S, White LL, Anderson KP, Medina E, Deutsch S, Ransom C, Jackson P, Kauffman TL, Mittendorf KF, Leo MC, Bulkley JE, Wilfond BS, Goddard KA, Feigelson HS. Evaluating cancer genetic services in a safety net system: overcoming barriers for a lasting impact beyond the CHARM research project. J Community Genet 2023:10.1007/s12687-023-00647-x. [PMID: 37126135 DOI: 10.1007/s12687-023-00647-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/14/2023] [Indexed: 05/02/2023] Open
Abstract
Underserved patients face substantial barriers to receiving cancer genetic services. The Cancer Health Assessments Reaching Many (CHARM) study evaluated ways to increase access to genetic testing for individuals in underserved populations at risk for hereditary cancer syndromes (HCS). Here, we report the successful implementation of CHARM in a low-resource environment and the development of sustainable processes to continue genetic risk assessment in this setting. The research team involved key clinical personnel and patient advisors at Denver Health to provide input on study methods and materials. Through iterative and collaborative stakeholder engagement, the team identified barriers and developed solutions that would both facilitate participation in CHARM and be feasible to implement and sustain long term in clinical care. With a focus on infrastructure building, educational modules were developed to increase awareness among referring providers, and standard methods of identifying and managing HCS patients were implemented in the electronic medical record. Three hundred sixty-four DH patients successfully completed the risk assessment tool within the study, and we observed a sustained increase in referrals to genetics for HCS (from 179 in 2017 to 427 in 2021 post-intervention). Implementation of the CHARM study at a low-resourced safety net health system resulted in sustainable improvements in access to cancer genetic risk assessment and services that continue even after the study ended.Trial registration NCT03426878.
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Affiliation(s)
- Sonia Okuyama
- Division of Oncology, Denver Health and Hospital Authority, Denver, CO, USA.
| | - Larissa L White
- Institute for Health Research, Kaiser Permanente, Aurora, CO, USA
| | | | - Elizabeth Medina
- Ambulatory Care Services, Denver Health and Hospital Authority, Denver, CO, USA
| | - Sonia Deutsch
- Ambulatory Care Services, Denver Health and Hospital Authority, Denver, CO, USA
| | | | - Paige Jackson
- Denver Health and Hospital Authority, Denver, CO, USA
| | - Tia L Kauffman
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | | | - Michael C Leo
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Katrina Ab Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR, USA
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
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12
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Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 2023; 25:100006. [PMID: 36621880 PMCID: PMC10085845 DOI: 10.1016/j.gim.2023.100006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk. METHODS To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results. RESULTS GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022. CONCLUSION Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Harris T Bland
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pedro J Caraballo
- Department of Internal Medicine and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ozan Dikilitas
- Mayo Clinician Investigator Training Program, Department of Internal Medicine and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alanna DiVietro
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Sophie Forman
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Adam S Gordon
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Richard Green
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | | | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sofia Labrecque
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Lori Orlando
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL
| | | | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Konrad Teodor Sawicki
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David Veenstra
- School of Pharmacy, University of Washington, Seattle, WA
| | - Digna R Velez Edwards
- Division of Quantitative Science, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - James Booth
- Department of Emergency Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - James J Cimino
- Division of General Internal Medicine and the Informatics Institute, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Patrick Davis
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Beth Devine
- School of Pharmacy, University of Washington, Seattle, WA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | | | - Melissa L Habrat
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Christin Hoell
- Department of Obstetrics & Gynecology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Martha Horike-Pyne
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eimear E Kenny
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Bruce Korf
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | | | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Thomas May
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA
| | | | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Brenda Mutai
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bahram Namjou
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Mass General Brigham Personalized Medicine, Boston, MA
| | - Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | | | - Maya Sabatello
- Division of Nephrology, Department of Medicine & Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York, NY
| | - Dan J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Baergen Schultz
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Lynn Seabolt
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Gabriel Q Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, AZ
| | - Richard R Sharp
- Biomedical Ethics Program, Department of Quantitative Health Science, Mayo Clinic, Rochester, MN
| | - Brian Shirts
- Department of Laboratory Medicine & Pathology, University of Washington Medical Center, Seattle, WA
| | - Maureen E Smith
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Jordan W Smoller
- Department of Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeritt Thayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Theresa Walunas
- Department of Medicine and Center for Health Information Partnerships, Northwestern University, Chicago, IL
| | - Wei-Qi Wei
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN.
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13
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Rahman P, Ye C, Mittendorf KF, Lenoue-Newton M, Micheel C, Wolber J, Osterman T, Fabbri D. Accelerated curation of checkpoint inhibitor-induced colitis cases from electronic health records. JAMIA Open 2023; 6:ooad017. [PMID: 37012912 PMCID: PMC10066800 DOI: 10.1093/jamiaopen/ooad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 03/01/2023] [Indexed: 04/04/2023] Open
Abstract
Objective Automatically identifying patients at risk of immune checkpoint inhibitor (ICI)-induced colitis allows physicians to improve patientcare. However, predictive models require training data curated from electronic health records (EHR). Our objective is to automatically identify notes documenting ICI-colitis cases to accelerate data curation. Materials and Methods We present a data pipeline to automatically identify ICI-colitis from EHR notes, accelerating chart review. The pipeline relies on BERT, a state-of-the-art natural language processing (NLP) model. The first stage of the pipeline segments long notes using keywords identified through a logistic classifier and applies BERT to identify ICI-colitis notes. The next stage uses a second BERT model tuned to identify false positive notes and remove notes that were likely positive for mentioning colitis as a side-effect. The final stage further accelerates curation by highlighting the colitis-relevant portions of notes. Specifically, we use BERT’s attention scores to find high-density regions describing colitis. Results The overall pipeline identified colitis notes with 84% precision and reduced the curator note review load by 75%. The segment BERT classifier had a high recall of 0.98, which is crucial to identify the low incidence (<10%) of colitis. Discussion Curation from EHR notes is a burdensome task, especially when the curation topic is complicated. Methods described in this work are not only useful for ICI colitis but can also be adapted for other domains. Conclusion Our extraction pipeline reduces manual note review load and makes EHR data more accessible for research.
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Affiliation(s)
- Protiva Rahman
- Corresponding Author: Protiva Rahman, Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End, Suite #1475, Nashville, TN 37203, USA;
| | - Cheng Ye
- Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathleen F Mittendorf
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michele Lenoue-Newton
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christine Micheel
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jan Wolber
- Pharmaceutical Diagnostics, GE Healthcare, Chalfont St Giles, UK
| | - Travis Osterman
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel Fabbri
- Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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14
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Ferket BS, Baldwin Z, Murali P, Pai A, Mittendorf KF, Russell HV, Chen F, Lynch FL, Lich KH, Hindorff LA, Savich R, Slavotinek A, Smith HS, Gelb BD, Veenstra DL. Cost-effectiveness frameworks for comparing genome and exome sequencing versus conventional diagnostic pathways: A scoping review and recommended methods. Genet Med 2022; 24:2014-2027. [PMID: 35833928 PMCID: PMC9997042 DOI: 10.1016/j.gim.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Methodological challenges have limited economic evaluations of genome sequencing (GS) and exome sequencing (ES). Our objective was to develop conceptual frameworks for model-based cost-effectiveness analyses (CEAs) of diagnostic GS/ES. METHODS We conducted a scoping review of economic analyses to develop and iterate with experts a set of conceptual CEA frameworks for GS/ES for prenatal testing, early diagnosis in pediatrics, diagnosis of delayed-onset disorders in pediatrics, genetic testing in cancer, screening of newborns, and general population screening. RESULTS Reflecting on 57 studies meeting inclusion criteria, we recommend the following considerations for each clinical scenario. For prenatal testing, performing comparative analyses of costs of ES strategies and postpartum care, as well as genetic diagnoses and pregnancy outcomes. For early diagnosis in pediatrics, modeling quality-adjusted life years (QALYs) and costs over ≥20 years for rapid turnaround GS/ES. For hereditary cancer syndrome testing, modeling cumulative costs and QALYs for the individual tested and first/second/third-degree relatives. For tumor profiling, not restricting to treatment uptake or response and including QALYs and costs of downstream outcomes. For screening, modeling lifetime costs and QALYs and considering consequences of low penetrance and GS/ES reanalysis. CONCLUSION Our frameworks can guide the design of model-based CEAs and ultimately foster robust evidence for the economic value of GS/ES.
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Affiliation(s)
- Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Zach Baldwin
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, University of Washington, Seattle, WA
| | - Akila Pai
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Heidi V Russell
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX; Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Flavia Chen
- Program in Bioethics, University of California San Francisco, San Francisco, CA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | | | - Kristen Hassmiller Lich
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Renate Savich
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS; Division of Neonatology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Bruce D Gelb
- Departments of Pediatrics and Genetics & Genomic Sciences, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David L Veenstra
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
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15
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Knerr S, Guo B, Mittendorf KF, Feigelson HS, Gilmore MJ, Jarvik GP, Kauffman TL, Keast E, Lynch FL, Muessig KR, Okuyama S, Veenstra DL, Zepp JM, Goddard KA, Devine B. Risk-reducing surgery in unaffected individuals receiving cancer genetic testing in an integrated health care system. Cancer 2022; 128:3090-3098. [PMID: 35679147 PMCID: PMC9308746 DOI: 10.1002/cncr.34349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Germline genetic testing enables primary cancer prevention, including through prophylactic surgery. We examined risk-reducing surgeries in unaffected individuals tested for hereditary cancer susceptibly between 2010 and 2018 in the Kaiser Permanente Northwest health system. METHODS We used an internal genetic testing database to create a cohort of individuals who received tests including one or more high-penetrance hereditary cancer susceptibility gene. We then identified, after testing, bilateral mastectomy, bilateral salpingo-oophorectomy (BSO), and total hysterectomy procedures in electronic health record and claims data through 2019. We describe surgery utilization by genetic test results and National Comprehensive Cancer Network (NCCN) guidelines. RESULTS The cohort included 1020 individuals, 16% with pathogenic/likely pathogenic (P/LP) variants in one or more of the following genes: BRCA1, BRCA2, CHEK2, APC, MUTYH, ATM, MSH2, PALB2, BRIP1, MLH1, MSH6, EPCAM, FLCN, RAD51C, RAD51D, or TP53. Among individuals with P/LP variants making them candidates for mastectomy, BSO, or hysterectomy per NCCN guidelines, 34% (33/97), 24% (23/94), and 8% (1/12), respectively, underwent surgery during follow-up. Fifty-three percent (18/37) of hysterectomies were among APC, BRCA1, and BRCA2 P/LP variant heterozygotes, typically concurrent with BSO. Three individuals with variants of uncertain significance (only) and 22 with negative results had prophylactic surgery after genetic testing. CONCLUSIONS Uptake of risk-reducing surgery following usual care genetic testing appears to be lower than in studies that actively recruit high-risk patients and provide testing and follow-up care in specialized settings. Factors in addition to genetic test results and NCCN guidelines motivate prophylactic surgery use and deserve further study.
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Affiliation(s)
- Sarah Knerr
- School of Public Health, University of Washington, Seattle, WA
| | - Boya Guo
- School of Public Health, University of Washington, Seattle, WA
| | - Kathleen F. Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | | | - Marian J. Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Gail P. Jarvik
- School of Medicine, University of Washington, Seattle, WA
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland OR
| | - Erin Keast
- Center for Health Research, Kaiser Permanente Northwest, Portland OR
| | - Frances L. Lynch
- Center for Health Research, Kaiser Permanente Northwest, Portland OR
| | - Kristin R. Muessig
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Sonia Okuyama
- Division of Oncology, Denver Health and Hospital Authority, Denver, CO
| | - David L. Veenstra
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
| | - Jamilyn M. Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Katrina A.B. Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Beth Devine
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
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16
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Lindberg NM, Mittendorf KF, Duenas DM, Anderson K, Koomas A, Kraft SA, Okuyama S, Shipman KJ, Vandermeer ML, Goddard KAB, Wilfond BS, McMullen C. Engaging Patient Advisory Committees to Inform a Genomic Cancer Risk Study: Lessons for Future Efforts. Perm J 2022; 26:28-39. [DOI: 10.7812/tpp/21.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nangel M Lindberg
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Devan M Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA, USA
| | | | - Alyssa Koomas
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA, USA
- Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Sonia Okuyama
- Denver Health and Hospital Authority, Denver, CO, USA
| | - Kelly J Shipman
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA, USA
- Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Katrina AB Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA, USA
- Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Carmit McMullen
- Kaiser Permanente Center for Health Research, Portland, OR, USA
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17
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Mittendorf KF, Lewis HS, Duenas DM, Eubanks DJ, Gilmore MJ, Goddard KAB, Joseph G, Kauffman TL, Kraft SA, Lindberg NM, Reyes AA, Shuster E, Syngal S, Ukaegbu C, Zepp JM, Wilfond BS, Porter KM. Literacy-adapted, electronic family history assessment for genetics referral in primary care: patient user insights from qualitative interviews. Hered Cancer Clin Pract 2022; 20:22. [PMID: 35689290 PMCID: PMC9188215 DOI: 10.1186/s13053-022-00231-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Risk assessment for hereditary cancer syndromes is recommended in primary care, but family history is rarely collected in enough detail to facilitate risk assessment and referral - a roadblock that disproportionately impacts individuals with healthcare access barriers. We sought to qualitatively assess a literacy-adapted, electronic patient-facing family history tool developed for use in diverse, underserved patient populations recruited in the Cancer Health Assessments Reaching Many (CHARM) Study. METHODS Interview participants were recruited from a subpopulation of CHARM participants who experienced barriers to tool use in terms of spending a longer time to complete the tool, having incomplete attempts, and/or providing inaccurate family history in comparison to a genetic counselor-collected standard. We conducted semi-structured interviews with participants about barriers and facilitators to tool use and overall tool acceptability; interviews were recorded and professionally transcribed. Transcripts were coded based on a codebook developed using inductive techniques, and coded excerpts were reviewed to identify overarching themes related to barriers and facilitators to family history self-assessment and acceptability of the study tool. RESULTS Interviewees endorsed the tool as easy to navigate and understand. However, they described barriers related to family history information, literacy and language, and certain tool functions. Participants offered concrete, easy-to-implement solutions to each barrier. Despite experience barriers to use of the tool, most participants indicated that electronic family history self-assessment was acceptable or preferable in comparison to clinician-collected family history. CONCLUSIONS Even for participants who experienced barriers to tool use, family history self-assessment was considered an acceptable alternative to clinician-collected family history. Barriers experienced could be overcome with minor adaptations to the current family history tool. TRIAL REGISTRATION This study is a sub-study of the Cancer Health Assessments Reaching Many (CHARM) trial, ClinicalTrials.gov, NCT03426878. Registered 8 February 2018.
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Affiliation(s)
- Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Nashville, TN, 37203, USA
| | - Hannah S Lewis
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA
| | - Devan M Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA
| | - Donna J Eubanks
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Katrina A B Goddard
- Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California San Francisco, 490 Illinois Street, 7th Floor, San Francisco, CA, 94143, USA
| | - Tia L Kauffman
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA.,Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE. Pacific St, Seattle, WA, 98195, USA
| | - Nangel M Lindberg
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Ana A Reyes
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Elizabeth Shuster
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Sapna Syngal
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA.,Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Chinedu Ukaegbu
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA.,Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE. Pacific St, Seattle, WA, 98195, USA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA.
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18
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Amendola LM, Shuster E, Leo MC, Dorschner MO, Rolf BA, Shirts BH, Gilmore MJ, Okuyama S, Zepp JM, Kauffman TL, Mittendorf KF, Bellcross C, Jenkins CL, Joseph G, Riddle L, Syngal S, Ukaegbu C, Goddard KAB, Wilfond BS, Jarvik GP. Laboratory-related outcomes from integrating an accessible delivery model for hereditary cancer risk assessment and genetic testing in populations with barriers to access. Genet Med 2022; 24:1196-1205. [PMID: 35305866 DOI: 10.1016/j.gim.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/02/2023] Open
Abstract
PURPOSE This study aimed to evaluate the laboratory-related outcomes of participants who were offered genomic testing based on cancer family history risk assessment tools. METHODS Patients from clinics that serve populations with access barriers, who are screened at risk for a hereditary cancer syndrome based on adapted family history collection tools (the Breast Cancer Genetics Referral Screening Tool and PREMM5), were offered exome-based panel testing for cancer risk and medically actionable secondary findings. We used descriptive statistics, electronic health record review, and inferential statistics to explore participant characteristics and results, consultations and actions related to pathogenic/likely pathogenic variants identified, and variables predicting category of findings, respectively. RESULTS Of all the participants, 87% successfully returned a saliva kit. Overall, 5% had a pathogenic/likely pathogenic cancer risk variant and 1% had a secondary finding. Almost all (14/15, 93%) participants completed recommended consultations with nongenetics providers after an average of 17 months. The recommended actions (eg, breast magnetic resonance imaging) were completed by 17 of 25 participants. Participant personal history of cancer and PREMM5 score were each associated with the category of findings (history and colon cancer finding, Fisher's exact P = .02; history and breast cancer finding, Fisher's exact P = .01; PREMM5TM score; and colon cancer finding, Fisher's exact P < .001). CONCLUSION This accessible model of hereditary cancer risk assessment and genetic testing yielded results that were often acted upon by patients and physicians.
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Affiliation(s)
- Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA.
| | - Elizabeth Shuster
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Michael C Leo
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Michael O Dorschner
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Department of Laboratory Medicine and Pathology, UW Medicine, University of Washington, Seattle, WA
| | - Bradley A Rolf
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Brian H Shirts
- Department of Laboratory Medicine and Pathology, UW Medicine, University of Washington, Seattle, WA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics (TAG), Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Sonia Okuyama
- Division of Hematology-Oncology, Denver Health and Hospital Authority, Denver, CO
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics (TAG), Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Tia L Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics (TAG), Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Cecilia Bellcross
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Charisma L Jenkins
- Department of Translational and Applied Genomics (TAG), Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California San Francisco, San Francisco, CA
| | - Leslie Riddle
- Department of Humanities and Social Sciences, University of California San Francisco, San Francisco, CA
| | - Sapna Syngal
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA; Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA
| | - Chinedu Ukaegbu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics (TAG), Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital, Seattle, WA; Division of Bioethics and Paliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
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19
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Mittendorf KF, Micheel C, LeNoue-Newton M, Rahman P, Fabbri D, Wolber J, Osterman TJ, Fouda M, Park BH. Overcoming barriers in academic-industry partnerships to improve predictive modeling in immuno-oncology. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e13581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13581 Background: In the past decade, immunotherapies have revolutionized oncology practice by prolonging patient survival in previously rapidly fatal cancers. However, severe immune toxicities present a challenge, affecting ̃20% and up to 50% of patients on immune monotherapies and combination immunotherapies, respectively. Oncologists must balance toxicity risk with potential efficacy, and pharmaceutical companies have a vested interest in selecting patients with the highest benefit–risk ratio during trial enrollment. Predictive toxicity–efficacy modeling has the potential to guide trial subject selection and clinical care, yet there remains a need for predictive models that can be practically implemented in these settings. Methods: A common academic–industry contract data–transfer framework—wherein academic medical institutions and industry counterparts act in isolation—creates barriers to development of high-quality algorithms with practical applications. In this framework, 1) academic medical institutions provide patient data as a “data dump;” these data are static and cannot be refined—reducing opportunities for quality control; 2) predictive model outcomes may include artifacts that are not identified; 3) manual curation of patient data is required to accurately replicate the model in real-world settings; and 4) lack of clinician participation reduces the potential clinical applications of models and reciprocal benefit to the academic institution. We outline a more contemporary, engaged approach to unite strengths of both partners to achieve a common goal. Results: In 2019, Vanderbilt University Medical Center and GE Healthcare partnered with the goal of enabling safer and more precise immunotherapy use. As part of this work, we formulated a recipe for academic–industry partnerships that offers unique advantages over a static contract framework. In our iterative, interactive approach, 1) clinical and curation experts meet with industry modelers to dynamically refine deidentified data sets by resolving discrepancies in data from different sources (e.g., manually curated vs. structured data); 2) clinical experts iteratively review outputs of predictive models to identify potential artifacts and refine final models; 3) expert curators iterate with in-house machine-learning experts to create algorithms to automate curation of natural language elements from the identified EHR data; and 4) clinical and industry stakeholders participate in regular meetings with modelers to ensure clinical and trial utility of the modeling approach. Conclusions: Compared to data transfer-only relationships, this partnership framework offers an opportunity to develop more informed, higher quality immunotherapy models with clinical and industry applications.
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Affiliation(s)
| | - Christine Micheel
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Michele LeNoue-Newton
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | | | | | - Jan Wolber
- GE Healthcare Ltd., Little Chalfont, United Kingdom
| | - Travis John Osterman
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | | | - Ben Ho Park
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
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20
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Muenzen KD, Amendola LM, Kauffman TL, Mittendorf KF, Bensen JT, Chen F, Green R, Powell BC, Kvale M, Angelo F, Farnan L, Fullerton SM, Robinson JO, Li T, Murali P, Lawlor JM, Ou J, Hindorff LA, Jarvik GP, Crosslin DR. Lessons learned and recommendations for data coordination in collaborative research: The CSER consortium experience. Human Genetics and Genomics Advances 2022; 3:100120. [PMID: 35707062 PMCID: PMC9190054 DOI: 10.1016/j.xhgg.2022.100120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Integrating data across heterogeneous research environments is a key challenge in multi-site, collaborative research projects. While it is important to allow for natural variation in data collection protocols across research sites, it is also important to achieve interoperability between datasets in order to reap the full benefits of collaborative work. However, there are few standards to guide the data coordination process from project conception to completion. In this paper, we describe the experiences of the Clinical Sequence Evidence-Generating Research (CSER) consortium Data Coordinating Center (DCC), which coordinated harmonized survey and genomic sequencing data from seven clinical research sites from 2020 to 2022. Using input from multiple consortium working groups and from CSER leadership, we first identify 14 lessons learned from CSER in the categories of communication, harmonization, informatics, compliance, and analytics. We then distill these lessons learned into 11 recommendations for future research consortia in the areas of planning, communication, informatics, and analytics. We recommend that planning and budgeting for data coordination activities occur as early as possible during consortium conceptualization and development to minimize downstream complications. We also find that clear, reciprocal, and continuous communication between consortium stakeholders and the DCC is equally important to maintaining a secure and centralized informatics ecosystem for pooling data. Finally, we discuss the importance of actively interrogating current approaches to data governance, particularly for research studies that straddle the research-clinical divide.
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21
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O'Daniel JM, Ackerman S, Desrosiers LR, Rego S, Knight SJ, Mollison L, Byfield G, Anderson KP, Danila MI, Horowitz CR, Joseph G, Lamoure G, Lindberg NM, McMullen CK, Mittendorf KF, Ramos MA, Robinson M, Sillari C, Madden EB. Integration of stakeholder engagement from development to dissemination in genomic medicine research: Approaches and outcomes from the CSER Consortium. Genet Med 2022; 24:1108-1119. [PMID: 35227608 PMCID: PMC9081226 DOI: 10.1016/j.gim.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
PURPOSE There is a critical need for genomic medicine research that reflects and benefits socioeconomically and ancestrally diverse populations. However, disparities in research populations persist, highlighting that traditional study designs and materials may be insufficient or inaccessible to all groups. New approaches can be gained through collaborations with patient/community stakeholders. Although some benefits of stakeholder engagement are recognized, routine incorporation into the design and implementation of genomics research has yet to be realized. METHODS The National Institutes of Health-funded Clinical Sequencing Evidence-Generating Research (CSER) consortium required stakeholder engagement as a dedicated project component. Each CSER project planned and carried out stakeholder engagement activities with differing goals and expected outcomes. Examples were curated from each project to highlight engagement strategies and outcomes throughout the research lifecycle from development through dissemination. RESULTS Projects tailored strategies to individual study needs, logistical constraints, and other challenges. Lessons learned include starting early with engagement efforts across project stakeholder groups and planned flexibility to enable adaptations throughout the project lifecycle. CONCLUSION Each CSER project used more than 1 approach to engage with relevant stakeholders, resulting in numerous adaptations and tremendous value added throughout the full research lifecycle. Incorporation of community stakeholder insight improves the outcomes and relevance of genomic medicine research.
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Affiliation(s)
- Julianne M O'Daniel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Sara Ackerman
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA
| | - Lauren R Desrosiers
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Shannon Rego
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Sara J Knight
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Lonna Mollison
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Grace Byfield
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Maria I Danila
- Division of Clinical Immunology and Rheumatology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California San Francisco, San Francisco, CA
| | - Grace Lamoure
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Nangel M Lindberg
- Center for Health Research Kaiser Permanente Northwest, Portland, OR
| | - Carmit K McMullen
- Center for Health Research Kaiser Permanente Northwest, Portland, OR
| | - Kathleen F Mittendorf
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Michelle A Ramos
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Catherine Sillari
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Ebony B Madden
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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22
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Rolf BA, Schneider JL, Amendola LM, Davis JV, Mittendorf KF, Schmidt MA, Jarvik GP, Wilfond BS, Goddard KAB, Hunter JE. Barriers to family history knowledge and family communication among LGBTQ+ individuals in the context of hereditary cancer risk assessment. J Genet Couns 2022; 31:230-241. [PMID: 34302314 PMCID: PMC8783924 DOI: 10.1002/jgc4.1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/15/2021] [Accepted: 06/26/2021] [Indexed: 02/03/2023]
Abstract
Openness about identity as lesbian, gay, bisexual, transgender, queer, and other sexual orientations and gender identities (LGBTQ+) may cause strain on relationships between family members, which could lead to limited knowledge of cancer family history and reduced communication with family members. As a result, members of the LGBTQ+ community may have more difficulty accessing genetic counseling services for inherited cancer risk. We applied a mixed-methods approach to explore potential barriers to knowledge of cancer family history and family communication among participants of the Cancer Health Assessments Reaching Many (CHARM) study who self-identified as LGBTQ+. We assessed perceptions of family functioning and communication of genetic test results to family members using survey tools and supplemented these data with 20 in-depth interviews to further assess participant perspectives and experiences. LGBTQ+ participants were more likely to report unhealthy family functioning on the survey tool, and some interviewees endorsed that openness about their LGBTQ+ identity led to strained family relationships and reduced communication about their family history of cancer. Overall, this study identified barriers that may be faced by members of the LGBTQ+ community which could limit their ability to access genetic counseling services for inherited cancer risk.
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Affiliation(s)
- Bradley A. Rolf
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | | | - Laura M. Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - James V. Davis
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Kathleen F. Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Mark A. Schmidt
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Gail P. Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Benjamin S. Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Katrina A. B. Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
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23
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Mittendorf KF, Kauffman TL, Amendola LM, Anderson KP, Biesecker BB, Dorschner MO, Duenas DM, Eubanks DJ, Feigelson HS, Gilmore MJ, Hunter JE, Joseph G, Kraft SA, Lee SSJ, Leo MC, Liles EG, Lindberg NM, Muessig KR, Okuyama S, Porter KM, Riddle LS, Rolf BA, Rope AF, Zepp JM, Jarvik GP, Wilfond BS, Goddard KA. Corrigendum to “Cancer Health Assessments Reaching Many (CHARM): A clinical trial assessing a multimodal cancer genetics services delivery program and its impact on diverse populations” [Contemporary Clinical Trials 106 (2021) 106432]. Contemp Clin Trials 2022; 114:106682. [DOI: 10.1016/j.cct.2022.106682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Mittendorf KF, Knerr S, Kauffman TL, Lindberg NM, Anderson KP, Feigelson HS, Gilmore MJ, Hunter JE, Joseph G, Kraft SA, Zepp JM, Syngal S, Wilfond BS, Goddard KAB. Systemic Barriers to Risk-Reducing Interventions for Hereditary Cancer Syndromes: Implications for Health Care Inequities. JCO Precis Oncol 2021; 5:PO.21.00233. [PMID: 34778694 PMCID: PMC8585306 DOI: 10.1200/po.21.00233] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kathleen F. Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Sarah Knerr
- School of Public Health, University of Washington, Seattle, WA
| | - Tia L. Kauffman
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Nangel M. Lindberg
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | | | | | - Marian J. Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, School of Medicine, San Francisco, CA
| | - Stephanie A. Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Jamilyn M. Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
| | - Sapna Syngal
- Dana Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Benjamin S. Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Katrina A. B. Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR
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25
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Holt ME, Mittendorf KF, LeNoue-Newton M, Jain NM, Anderson I, Lovly CM, Osterman T, Micheel C, Levy M. My Cancer Genome: Coevolution of Precision Oncology and a Molecular Oncology Knowledgebase. JCO Clin Cancer Inform 2021; 5:995-1004. [PMID: 34554823 PMCID: PMC8807017 DOI: 10.1200/cci.21.00084] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The My Cancer Genome (MCG) knowledgebase and resulting website were launched in 2011 with the purpose of guiding clinicians in the application of genomic testing results for treatment of patients with cancer. Both knowledgebase and website were originally developed using a wiki-style approach that relied on manual evidence curation and synthesis of that evidence into cancer-related biomarker, disease, and pathway pages on the website that summarized the literature for a clinical audience. This approach required significant time investment for each page, which limited website scalability as the field advanced. To address this challenge, we designed and used an assertion-based data model that allows the knowledgebase and website to expand with the field of precision oncology. METHODS Assertions, or computationally accessible cause and effect statements, are both manually curated from primary sources and imported from external databases and stored in a knowledge management system. To generate pages for the MCG website, reusable templates transform assertions into reconfigurable text and visualizations that form the building blocks for automatically updating disease, biomarker, drug, and clinical trial pages. RESULTS Combining text and graph templates with assertions in our knowledgebase allows generation of web pages that automatically update with our knowledgebase. Automated page generation empowers rapid scaling of the website as assertions with new biomarkers and drugs are added to the knowledgebase. This process has generated more than 9,100 clinical trial pages, 18,100 gene and alteration pages, 900 disease pages, and 2,700 drug pages to date. CONCLUSION Leveraging both computational and manual curation processes in combination with reusable templates empowers automation and scalability for both the MCG knowledgebase and MCG website.
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Affiliation(s)
| | | | | | - Neha M Jain
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | | | | | | | | | - Mia Levy
- Rush University Medical Center, Chicago, IL
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26
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Lindberg NM, Gutierrez AM, Mittendorf KF, Ramos MA, Anguiano B, Angelo F, Joseph G. Creating accessible Spanish language materials for Clinical Sequencing Evidence-Generating Research consortium genomic projects: challenges and lessons learned. Per Med 2021; 18:441-454. [PMID: 34448595 PMCID: PMC8438935 DOI: 10.2217/pme-2020-0075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/26/2021] [Indexed: 01/31/2023]
Abstract
Aim: To increase Spanish speakers' representation in genomics research, accessible study materials on genetic topics must be made available in Spanish. Materials & methods: The Clinical Sequencing Evidence-Generating Research consortium is evaluating genome sequencing for underserved populations. All sites needed Spanish translation of recruitment materials, surveys and return of results. Results: We describe our process for translating site-specific materials, as well as shared measures across sites, to inform future efforts to engage Spanish speakers in research. Conclusion: In translating and adapting study materials for roughly 1000 Spanish speakers across the USA, and harmonizing translated measures across diverse sites, we overcame numerous challenges. Translation should be performed by professionals. Studies must allocate sufficient time, effort and budget to translate and adapt participant materials.
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Affiliation(s)
- Nangel M Lindberg
- Kaiser Permanente Northwest Center for Health Research, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Amanda M Gutierrez
- Baylor College of Medicine Center for Medical Ethics & Health Policy, One Baylor Plaza, Suite 310D, Houston, TX 77030, USA
| | - Kathleen F Mittendorf
- Kaiser Permanente Northwest Center for Health Research, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Michelle A Ramos
- Department of Population Health Science & Policy Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1077, New York, NY 10029, USA
| | - Beatriz Anguiano
- University of California, San Francisco (UCSF) Program in Bioethics, 3333 California Ave (suite 340), San Francisco, CA 94606, USA
| | - Frank Angelo
- CSER Coordinating Center, University of Washington, Division of Medical Genetics, Health Sciences Building, K-253 Box 357720 Seattle, WA 98195, USA
| | - Galen Joseph
- University of California San Francisco Department of Humanities & Social Sciences, 1450 3rd Street, Rm. 551 San Francisco, CA 94143, USA
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27
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Mittendorf KF, Kauffman TL, Amendola LM, Anderson KP, Biesecker BB, Dorschner MO, Duenas DM, Eubanks DJ, Feigelson HS, Gilmore MJ, Hunter JE, Joseph G, Kraft SA, Lee SSJ, Leo MC, Liles EG, Lindberg NM, Muessig KR, Okuyama S, Porter KM, Riddle LS, Rolf BA, Rope AF, Zepp JM, Jarvik GP, Wilfond BS, Goddard KAB. Cancer Health Assessments Reaching Many (CHARM): A clinical trial assessing a multimodal cancer genetics services delivery program and its impact on diverse populations. Contemp Clin Trials 2021; 106:106432. [PMID: 33984519 PMCID: PMC8336568 DOI: 10.1016/j.cct.2021.106432] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Advances in the application of genomic technologies in clinical care have the potential to increase existing healthcare disparities. Studies have consistently shown that only a fraction of eligible patients with a family history of cancer receive recommended cancer genetic counseling and subsequent genetic testing. Care delivery models using pre-test and post-test counseling are not scalable, which contributes to barriers in accessing genetics services. These barriers are even more pronounced for patients in historically underserved populations. We have designed a multimodal intervention to improve subsequent cancer surveillance, by improving the identification of patients at risk for familial cancer syndromes, reducing barriers to genetic counseling/testing, and increasing patient understanding of complex genetic results. We are evaluating this intervention in two large, integrated healthcare systems that serve diverse patient populations (NCT03426878). The primary outcome is the number of diagnostic (hereditary cancer syndrome) findings. We are examining the clinical and personal utility of streamlined pathways to genetic testing using electronic medical record data, surveys, and qualitative interviews. We will assess downstream care utilization of individuals receiving usual clinical care vs. genetic testing through the study. We will evaluate the impacts of a literacy-focused genetic counseling approach versus usual care genetic counseling on care utilization and participant understanding, satisfaction, and family communication. By recruiting participants belonging to historically underserved populations, this study is uniquely positioned to evaluate the potential of a novel genetics care delivery program to reduce care disparities.
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Affiliation(s)
- Kathleen F Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA.
| | - Tia L Kauffman
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA.
| | - Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | | | | | - Michael O Dorschner
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Devan M Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA
| | - Donna J Eubanks
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Heather Spencer Feigelson
- Institute for Health Research, Kaiser Permanente Colorado, 2550 S Parker Rd, Suite 200, Aurora, CO 80014, USA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, 1450 3rd Street, Rm 551 & 556, San Francisco, CA 94143, USA
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA; Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Sandra Soo Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, 630 West 168(th) St, PH15E-1525, New York, NY 10032, USA
| | - Michael C Leo
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Elizabeth G Liles
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Nangel M Lindberg
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Kristin R Muessig
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Sonia Okuyama
- Denver Health and Hospital Authority, 777 Bannock Denver, CO 80204, USA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA
| | - Leslie S Riddle
- Department of Humanities and Social Sciences, University of California, San Francisco, 1450 3rd Street, Rm 551 & 556, San Francisco, CA 94143, USA
| | - Bradley A Rolf
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Alan F Rope
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA; Genome Medical, 701 Gateway Blvd, Suite 380, San Francisco, CA 94080, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA; Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
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Jain N, Mittendorf KF, Holt M, Lenoue-Newton M, Maurer I, Miller C, Stachowiak M, Botyrius M, Cole J, Micheel C, Levy M. The My Cancer Genome clinical trial data model and trial curation workflow. J Am Med Inform Assoc 2021; 27:1057-1066. [PMID: 32483629 PMCID: PMC7647323 DOI: 10.1093/jamia/ocaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/07/2020] [Accepted: 04/17/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE As clinical trials evolve in complexity, clinical trial data models that can capture relevant trial data in meaningful, structured annotations and computable forms are needed to support accrual. MATERIAL AND METHODS We have developed a clinical trial information model, curation information system, and a standard operating procedure for consistent and accurate annotation of cancer clinical trials. Clinical trial documents are pulled into the curation system from publicly available sources. Using a web-based interface, a curator creates structured assertions related to disease-biomarker eligibility criteria, therapeutic context, and treatment cohorts by leveraging our data model features. These structured assertions are published on the My Cancer Genome (MCG) website. RESULTS To date, over 5000 oncology trials have been manually curated. All trial assertion data are available for public view on the MCG website. Querying our structured knowledge base, we performed a landscape analysis to assess the top diseases, biomarker alterations, and drugs featured across all cancer trials. DISCUSSION Beyond curating commonly captured elements, such as disease and biomarker eligibility criteria, we have expanded our model to support the curation of trial interventions and therapeutic context (ie, neoadjuvant, metastatic, etc.), and the respective biomarker-disease treatment cohorts. To the best of our knowledge, this is the first effort to capture these fields in a structured format. CONCLUSION This paper makes a significant contribution to the field of biomedical informatics and knowledge dissemination for precision oncology via the MCG website. KEY WORDS knowledge representation, My Cancer Genome, precision oncology, knowledge curation, cancer informatics, clinical trial data model.
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Affiliation(s)
- Neha Jain
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathleen F Mittendorf
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marilyn Holt
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michele Lenoue-Newton
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | | | | | | | - Christine Micheel
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mia Levy
- Department of Internal Medicine, Division of Hematology/Oncology, Rush University Medical Center, Chicago, Illinois, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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29
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Mittendorf KF, Ukaegbu C, Gilmore MJ, Lindberg NM, Kauffman TL, Eubanks DJ, Shuster E, Allen J, McMullen C, Feigelson HS, Anderson KP, Leo MC, Hunter JE, Sasaki SO, Zepp JM, Syngal S, Wilfond BS, Goddard KAB. Adaptation and early implementation of the PREdiction model for gene mutations (PREMM 5™) for lynch syndrome risk assessment in a diverse population. Fam Cancer 2021; 21:167-180. [PMID: 33754278 PMCID: PMC8458476 DOI: 10.1007/s10689-021-00243-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/04/2021] [Indexed: 01/20/2023]
Abstract
Lynch syndrome (LS) is the most common inherited cause of colorectal and endometrial cancers. Identifying individuals at risk for LS without personal cancer history requires detailed collection and assessment of family health history. However, barriers exist to family health history collection, especially in historically underserved populations. To improve LS risk assessment in historically underserved populations, we adapted the provider-facing PREdiction Model for gene Mutations (PREMM5™ model), a validated LS risk assessment model, into a patient-facing electronic application through an iterative development process involving expert and patient stakeholders. We report on preliminary findings based on the first 500 individuals exposed to the adapted application in a primary care population enriched for low-literacy and low-resource patients. Major adaptations to the PREMM5™ provider module included reduction in reading level, addition of interactive literacy aids, incorporation of family history assessment for both maternal and paternal sides of the family, and inclusion of questions about individual relatives or small groups of relatives to reduce cognitive burden. In the first 500 individuals, 90% completed the PREMM5™ independently; of those, 94% did so in 5 min or less (ranged from 0.2 to 48.8 min). The patient-facing application was able to accurately classify 84% of patients as having clinically significant or not clinically significant LS risk. Our preliminary results suggest that in this diverse study population, most participants were able to rapidly, accurately, and independently complete an interactive application collecting family health history assessment that accurately assessed for Lynch syndrome risk.
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Affiliation(s)
- Kathleen F Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA.
| | - Chinedu Ukaegbu
- Dana Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Nangel M Lindberg
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Tia L Kauffman
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Donna J Eubanks
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Elizabeth Shuster
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Jake Allen
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Carmit McMullen
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | | | | | - Michael C Leo
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | | | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | - Sapna Syngal
- Dana Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, Seattle, WA, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
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30
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Kraft SA, Porter KM, Duenas DM, Guerra C, Joseph G, Lee SSJ, Shipman KJ, Allen J, Eubanks D, Kauffman TL, Lindberg NM, Anderson K, Zepp JM, Gilmore MJ, Mittendorf KF, Shuster E, Muessig KR, Arnold B, Goddard KAB, Wilfond BS. Participant Reactions to a Literacy-Focused, Web-Based Informed Consent Approach for a Genomic Implementation Study. AJOB Empir Bioeth 2021; 12:1-11. [PMID: 32981477 PMCID: PMC7785634 DOI: 10.1080/23294515.2020.1823907] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Clinical genomic implementation studies pose challenges for informed consent. Consent forms often include complex language and concepts, which can be a barrier to diverse enrollment, and these studies often blur traditional research-clinical boundaries. There is a move toward self-directed, web-based research enrollment, but more evidence is needed about how these enrollment approaches work in practice. In this study, we developed and evaluated a literacy-focused, web-based consent approach to support enrollment of diverse participants in an ongoing clinical genomic implementation study. Methods: As part of the Cancer Health Assessments Reaching Many (CHARM) study, we developed a web-based consent approach that featured plain language, multimedia, and separate descriptions of clinical care and research activities. CHARM offered clinical exome sequencing to individuals at high risk of hereditary cancer. We interviewed CHARM participants about their reactions to the consent approach. We audio recorded, transcribed, and coded interviews using a deductively and inductively derived codebook. We reviewed coded excerpts as a team to identify overarching themes. Results: We conducted 32 interviews, including 12 (38%) in Spanish. Most (69%) enrolled without assistance from study staff, usually on a mobile phone. Those who completed enrollment in one day spent an average of 12 minutes on the consent portion. Interviewees found the information simple to read but comprehensive, were neutral to positive about the multimedia support, and identified increased access to testing in the study as the key difference from clinical care. Conclusions: This study showed that interviewees found our literacy-focused, web-based consent approach acceptable; did not distinguish the consent materials from other online study processes; and valued getting access to testing in the study. Overall, conducting empirical bioethics research in an ongoing clinical trial was useful to demonstrate the acceptability of our novel consent approach but posed practical challenges.
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Affiliation(s)
- Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, and Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, Washington, USA
| | - Devan M Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, Washington, USA
| | - Claudia Guerra
- Department of Anthropology, History and Social Medicine, University of California, San Francisco, California, USA
| | - Galen Joseph
- Department of Anthropology, History and Social Medicine, University of California, San Francisco, California, USA
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, New York, USA
| | - Kelly J Shipman
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, Washington, USA
| | - Jake Allen
- IT (Information Technology) Department, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Donna Eubanks
- IT (Information Technology) Department, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Tia L Kauffman
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Nangel M Lindberg
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | | | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Elizabeth Shuster
- Research Data and Analysis Center, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Kristin R Muessig
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Briana Arnold
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Northwest, Center for Health Research, Portland, Oregon, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, and Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
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Feigelson HS, Mittendorf KF, Kauffman TL, Anderson K, Okuyama S, Wilfond B, Jarvik GP, Amendola LM, McMullen C, Lynch F, Eubanks D, Shuster E, Allen J, Kraft SA, Joseph G, Lee SSJ, Goddard KA. Abstract PR02: Using web-based tools to assess familial cancer risk in diverse populations. Cancer Epidemiol Biomarkers Prev 2020. [DOI: 10.1158/1538-7755.modpop19-pr02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Introduction: The Cancer Health Risk Assessments Reaching Many (CHARM) study (NCT03426878) aims to increase access to genetic testing for hereditary cancer in low-income, low-literacy, and minority populations (hereafter referred to as “underserved”). To implement the study, we have capitalized on the availability of electronic medical record (EMR) systems, developed innovative web-based tools, and designed a novel telemedicine protocol for return of clinical genetic testing results.
Methods: Patients aged 18-49 years are recruited from two centers: Kaiser Permanente Northwest (KPNW; an integrated health care system in Portland, OR) and Denver Health (DH; a federally qualified health care center in Denver, CO). Specific protocols were developed to identify potentially eligible patients from the EMR and invite them to complete a web-based family history assessment. KPNW patients were recruited using email, text messaging, and in-clinic booths; DH patients were recruited via mail, phone, and provider referral. Validated risk assessment tools for Lynch syndrome (PREMM5) and heredity breast and ovarian cancer syndrome (B-RST) were adapted for our low-literacy and bilingual (English and Spanish) target population. Genetic testing is offered to patients with greater than average risk for hereditary cancer, or where risk cannot be assessed because of unknown family history or limited family structure. Eligible patients review a multipart, multimedia online consent. Those who consent to participate provide a saliva sample for clinical exome sequencing. Genetic counselors return results by telephone using traditional (usual care active comparator) or modified, communication-focused (experimental) counseling for pathogenic variants, likely pathogenic variants, and select variants of uncertain significance in 39 genes related to cancer risk, pathogenic variants in 79 genes related to medically actionable secondary findings, and 14 genes related to carrier status.
Results: In the first four months of recruitment, 258 patients have completed the risk assessment tool (48% are underserved). Of those, 180 (70%) had greater than average risk of hereditary cancer (or limited family history information) and were invited to participate (53% were underserved); 86% of underserved patients and 78% of patients who do not meet criteria for the underserved category have consented. The vast majority of participants complete enrollment without assistance from study staff, and in-person visits are not required for participation. Telephone genetic test result disclosure will begin in December 2018.
Conclusions: We have successfully developed online tools for cancer risk assessment that are accessible to underserved and low-literacy populations. These tools may be a cost-effective approach for improving the capture of family history data in the EMR. It does not require a provider to gather the information and the patient gets immediate feedback on results of the risk assessment and appropriate next steps.
This abstract is also being presented as Poster A37.
Citation Format: Heather Spencer Feigelson, Kathleen F. Mittendorf, Tia L. Kauffman, Katherine Anderson, Sonia Okuyama, Benjamin Wilfond, Gail P. Jarvik, Laura M. Amendola, Carmit McMullen, Fances Lynch, Donna Eubanks, Elizabeth Shuster, Jake Allen, Stephanie A. Kraft, Galen Joseph, Sandra Soo-Jin Lee, Katrina A.B. Goddard. Using web-based tools to assess familial cancer risk in diverse populations [abstract]. In: Proceedings of the AACR Special Conference on Modernizing Population Sciences in the Digital Age; 2019 Feb 19-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(9 Suppl):Abstract nr PR02.
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Affiliation(s)
| | | | - Tia L. Kauffman
- 2Kaiser Permanente Center for Health Research, Portland, OR,
| | | | | | | | | | | | - Carmit McMullen
- 2Kaiser Permanente Center for Health Research, Portland, OR,
| | - Fances Lynch
- 2Kaiser Permanente Center for Health Research, Portland, OR,
| | - Donna Eubanks
- 2Kaiser Permanente Center for Health Research, Portland, OR,
| | | | - Jake Allen
- 2Kaiser Permanente Center for Health Research, Portland, OR,
| | | | - Galen Joseph
- 6University of California, San Francisco, San Francisco, CA,
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Hutchison JM, Shih KC, Scheidt HA, Fantin SM, Parson KF, Pantelopulos GA, Harrington HR, Mittendorf KF, Qian S, Stein RA, Collier SE, Chambers MG, Katsaras J, Voehler MW, Ruotolo BT, Huster D, McFeeters RL, Straub JE, Nieh MP, Sanders CR. Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins. J Am Chem Soc 2020; 142:12715-12729. [PMID: 32575981 DOI: 10.1021/jacs.0c04669] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
How the distinctive lipid composition of mammalian plasma membranes impacts membrane protein structure is largely unexplored, partly because of the dearth of isotropic model membrane systems that contain abundant sphingolipids and cholesterol. This gap is addressed by showing that sphingomyelin and cholesterol-rich (SCOR) lipid mixtures with phosphatidylcholine can be cosolubilized by n-dodecyl-β-melibioside to form bicelles. Small-angle X-ray and neutron scattering, as well as cryo-electron microscopy, demonstrate that these assemblies are stable over a wide range of conditions and exhibit the bilayered-disc morphology of ideal bicelles even at low lipid-to-detergent mole ratios. SCOR bicelles are shown to be compatible with a wide array of experimental techniques, as applied to the transmembrane human amyloid precursor C99 protein in this medium. These studies reveal an equilibrium between low-order oligomer structures that differ significantly from previous experimental structures of C99, providing an example of how ordered membranes alter membrane protein structure.
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Affiliation(s)
- James M Hutchison
- Chemical and Physical Biology Graduate Program and Center for Structural Biology, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - Kuo-Chih Shih
- Polymer Program, Department of Chemical & Biomolecular Engineering, and Department of Biomedical Engineering, University of Connecticut, Storrs 06269, Connecticut, United States
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig 16-18, 04107, Germany
| | - Sarah M Fantin
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - George A Pantelopulos
- Department of Chemistry, Boston University, Boston 02215, Massachusetts, United States
| | - Haley R Harrington
- Center for Structural Biology and Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville 37240, Tennessee, United States
| | - Kathleen F Mittendorf
- Center for Health Research, Kaiser Permanente, Portland 97227, Oregon, United States
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge 37831, Tennessee, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville37240, Tennessee, United States
| | - Scott E Collier
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland 97227, Oregon, United States
| | - Melissa G Chambers
- Center for Structural Biology, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - John Katsaras
- Neutron Scattering Division and Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge 37831, Tennessee, United States
| | - Markus W Voehler
- Center for Structural Biology and Department of Chemistry, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig 16-18, 04107, Germany
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama, Huntsville 35899, Alabama, United States
| | - John E Straub
- Department of Chemistry, Boston University, Boston 02215, Massachusetts, United States
| | - Mu-Ping Nieh
- Polymer Program, Department of Chemical & Biomolecular Engineering, and Department of Biomedical Engineering, University of Connecticut, Storrs 06269, Connecticut, United States
| | - Charles R Sanders
- Center for Structural Biology, Department of Biochemistry, and Department of Medicine, Vanderbilt University School of Medicine, Nashville 37240, Tennessee, United States
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Mittendorf KF, Hunter JE, Schneider JL, Shuster E, Rope AF, Zepp J, Gilmore MJ, Muessig KR, Davis JV, Kauffman TL, Bergen KM, Wiesner GL, Acheson LS, Peterson SK, Syngal S, Reiss JA, Goddard KAB. Recommended care and care adherence following a diagnosis of Lynch syndrome: a mixed-methods study. Hered Cancer Clin Pract 2019; 17:31. [PMID: 31890059 PMCID: PMC6915941 DOI: 10.1186/s13053-019-0130-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) syndrome. This study assesses trends in diagnosis of LS and adherence to recommended LS-related care in a large integrated healthcare organization (~ 575,000 members). METHODS Electronic medical record (EMR) data (1999-2015) were examined to identify patients with a diagnosis of LS. We examined their LS-associated care recommendations and adherence to these recommendations. Qualitative patient and provider interviews were conducted with the aim of identifying opportunities for improved care delivery. RESULTS We identified 74 patients with a diagnosis of LS; 64% were diagnosed with a LS-related malignancy prior to their diagnosis of LS. The time to LS diagnosis following development of a LS-related cancer decreased over time: before 2009 11% of individuals received a diagnosis of LS within 1 year of developing a LS-related cancer compared to 83% after 2009 (p < 0.0001). Colonoscopy recommendations were documented in the EMR for almost all patients with LS (96%). Documentation of other recommendations for cancer surveillance was less commonly found. Overall, patient adherence to colonoscopy was high (M = 81.5%; SD = 32.7%), and adherence to other recommendations varied. To improve care coordination, patients and providers suggested providing automated reminder prompts for LS-related surveillance, adding a LS-specific diagnosis code, and providing guidelines for LS-related surveillance in the EMR. CONCLUSIONS We identified fewer than expected patients with LS in our large care system, indicating that there is still a diagnostic care gap. However, patients with LS were likely to receive and follow CRC surveillance recommendations. Recommendations for and adherence to extracolonic surveillance were variable. Improved care coordination and clearer documentation of the LS diagnosis is needed.
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Affiliation(s)
- Kathleen F. Mittendorf
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Jessica Ezzell Hunter
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Jennifer L. Schneider
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Elizabeth Shuster
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Alan F. Rope
- Northwest Permanente, Kaiser Permanente Northwest, Portland, OR USA
| | - Jamilyn Zepp
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR USA
| | - Marian J. Gilmore
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR USA
| | - Kristin R. Muessig
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - James V. Davis
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Kellene M. Bergen
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Georgia L. Wiesner
- Vanderbilt Hereditary Cancer Program, Vanderbilt University Medical Center, Nashville, TN USA
| | - Louise S. Acheson
- Case Western Reserve University, University Hospitals Cleveland Medical Center, Cleveland, OH USA
| | | | - Sapna Syngal
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Jacob A. Reiss
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
| | - Katrina A. B. Goddard
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Avenue, Portland, OR 97227 USA
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Webber EM, Hunter JE, Biesecker LG, Buchanan AH, Clarke EV, Currey E, Dagan-Rosenfeld O, Lee K, Lindor NM, Martin CL, Milosavljevic A, Mittendorf KF, Muessig KR, O'Daniel JM, Patel RY, Ramos EM, Rego S, Slavotinek AM, Sobriera NLM, Weaver MA, Williams MS, Evans JP, Goddard KAB. Evidence-based assessments of clinical actionability in the context of secondary findings: Updates from ClinGen's Actionability Working Group. Hum Mutat 2019; 39:1677-1685. [PMID: 30311382 PMCID: PMC6211797 DOI: 10.1002/humu.23631] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/19/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
The use of genome-scale sequencing allows for identification of genetic findings beyond the original indication for testing (secondary findings). The ClinGen Actionability Working Group's (AWG) protocol for evidence synthesis and semi-quantitative metric scoring evaluates four domains of clinical actionability for potential secondary findings: severity and likelihood of the outcome, and effectiveness and nature of the intervention. As of February 2018, the AWG has scored 127 genes associated with 78 disorders (up-to-date topics/scores are available at www.clinicalgenome.org). Scores across these disorders were assessed to compare genes/disorders recommended for return as secondary findings by the American College of Medical Genetics and Genomics (ACMG) with those not currently recommended. Disorders recommended by the ACMG scored higher on outcome-related domains (severity and likelihood), but not on intervention-related domains (effectiveness and nature of the intervention). Current practices indicate that return of secondary findings will expand beyond those currently recommended by the ACMG. The ClinGen AWG evidence reports and summary scores are not intended as classifications of actionability, rather they provide a resource to aid decision makers as they determine best practices regarding secondary findings. The ClinGen AWG is working with the ACMG Secondary Findings Committee to update future iterations of their secondary findings list.
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Affiliation(s)
- Elizabeth M Webber
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | | | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Adam H Buchanan
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Elizabeth V Clarke
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Erin Currey
- Division of Genomics and Society, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Kristy Lee
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | - Kristin R Muessig
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Erin M Ramos
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Shannon Rego
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Anne M Slavotinek
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Nara Lygia M Sobriera
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - James P Evans
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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Paquin RS, Mittendorf KF, Lewis MA, Hunter JE, Lee K, Berg JS, Williams MS, Goddard KAB. Expert and lay perspectives on burden, risk, tolerability, and acceptability of clinical interventions for genetic disorders. Genet Med 2019; 21:2561-2568. [PMID: 31028355 DOI: 10.1038/s41436-019-0524-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/15/2019] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The Clinical Genome Resource (ClinGen) Actionability Working Group (AWG) developed a semiquantitative scoring metric to rate clinical actionability of genetic disorders and associated genes in four domains: (1) severity of the outcome, (2) likelihood of the outcome, (3) effectiveness of the intervention to prevent/minimize the outcome, and (4) nature of the intervention with respect to burden, risk, tolerability, and acceptability to the patient. This study aimed to assess whether nature of the intervention scores assigned by AWG experts reflected lay perceptions of intervention burden, risk, tolerability, and acceptability given the subjectivity of this domain. METHODS In July 2017, a general population sample of 1344 adults completed the study. Each participant was asked to read 1 of 24 plain language medical intervention synopses and answer questions related to its burden, risk, tolerability, and acceptability. We conducted three multilevel mixed model analyses predicting the perceived burden, perceived risk, and perceived overall nature of the intervention. RESULTS As AWG nature of the intervention scores increased, lay perceptions of intervention burden and risk decreased, and perceptions of tolerability and acceptability increased. CONCLUSION The findings show alignment between the ClinGen actionability scoring metric and lay perceptions of the nature of the intervention.
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Affiliation(s)
- Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC, USA.
| | | | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC, USA
| | | | - Kristy Lee
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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Naleway AL, Mittendorf KF, Irving SA, Henninger ML, Crane B, Smith N, Daley MF, Gee J. Primary Ovarian Insufficiency and Adolescent Vaccination. Pediatrics 2018; 142:peds.2018-0943. [PMID: 30131438 PMCID: PMC6719304 DOI: 10.1542/peds.2018-0943] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Published case series have suggested a potential association between human papillomavirus (HPV) vaccination and primary ovarian insufficiency (POI). We describe POI incidence and estimate POI risk after HPV; tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis, adsorbed (Tdap); inactivated influenza (II); and meningococcal conjugate (MenACWY) vaccination. METHODS We searched Kaiser Permanente Northwest electronic health records for outpatient diagnoses suggestive of POI in female patients aged 11 to 34 years between 2006 and 2014. We reviewed and adjudicated the medical record to confirm diagnoses and estimate symptom onset dates. We excluded cases with known causes and calculated the incidence of idiopathic POI. We estimated risk by calculating hazard ratios and 95% confidence intervals (CIs). RESULTS From a cohort of 199 078 female patients, we identified 120 with diagnoses suggestive of POI. After adjudication and exclusion of 26 POI cases with known causes, we confirmed 46 idiopathic POI cases. POI incidence was low in 11- to 14-year-olds (0.87 per 1 000 000 person-months) and increased with age. One confirmed case patient received the HPV vaccine 23 months before the first clinical evaluation for delayed menarche. The adjusted hazard ratio was 0.30 (95% CI: 0.07-1.36) after HPV, 0.88 (95% CI: 0.37-2.10) after Tdap, 1.42 (95% CI: 0.59-3.41) after II, and 0.94 (95% CI: 0.27-3.23) after MenACWY vaccination. CONCLUSIONS We did not find a statistically significant elevated risk of POI after HPV, Tdap, II, or MenACWY vaccination in this population-based retrospective cohort study. These findings should lessen concern about POI risk after adolescent vaccination.
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Affiliation(s)
- Allison L. Naleway
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | | | | | | | - Bradley Crane
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Ning Smith
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Matthew F. Daley
- Institute for Health Research, Kaiser Permanente Colorado, Denver, Colorado;,Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado
| | - Julianne Gee
- Immunization Safety Office, Centers for Disease Control and Prevention, Atlanta, Georgia
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Mittendorf KF, Marinko JT, Hampton CM, Ke Z, Hadziselimovic A, Schlebach JP, Law CL, Li J, Wright ER, Sanders CR, Ohi MD. Peripheral myelin protein 22 alters membrane architecture. Sci Adv 2017; 3:e1700220. [PMID: 28695207 PMCID: PMC5498104 DOI: 10.1126/sciadv.1700220] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/19/2017] [Indexed: 05/10/2023]
Abstract
Peripheral myelin protein 22 (PMP22) is highly expressed in myelinating Schwann cells of the peripheral nervous system. PMP22 genetic alterations cause the most common forms of Charcot-Marie-Tooth disease (CMTD), which is characterized by severe dysmyelination in the peripheral nerves. However, the functions of PMP22 in Schwann cell membranes remain unclear. We demonstrate that reconstitution of purified PMP22 into lipid vesicles results in the formation of compressed and cylindrically wrapped protein-lipid vesicles that share common organizational traits with compact myelin of peripheral nerves in vivo. The formation of these myelin-like assemblies depends on the lipid-to-PMP22 ratio, as well as on the PMP22 extracellular loops. Formation of the myelin-like assemblies is disrupted by a CMTD-causing mutation. This study provides both a biochemical assay for PMP22 function and evidence that PMP22 directly contributes to membrane organization in compact myelin.
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Affiliation(s)
- Kathleen F. Mittendorf
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Justin T. Marinko
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Cheri M. Hampton
- Division of Infectious Disease, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zunlong Ke
- Division of Infectious Disease, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Arina Hadziselimovic
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Jonathan P. Schlebach
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Cheryl L. Law
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Jun Li
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elizabeth R. Wright
- Division of Infectious Disease, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Corresponding author. (M.D.O.); (C.R.S.)
| | - Melanie D. Ohi
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
- Corresponding author. (M.D.O.); (C.R.S.)
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Levy MA, Osterman TJ, Jain N, Mittendorf KF, Micheel C. Utility of adding clinical data to a molecular results portal for improving clinical trial prescreening efficiency. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e18182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e18182 Background: Bioportals that aggregate patient genomic results and diagnosis data elements can be used as a tool for identifying potentially eligible patients for molecularly-driven clinical trials. However, over time, increasing numbers of patients will be deceased, making this process less efficient. Methods: We sought to evaluate the addition of minimal clinical data to a clinical trial prescreening workflow utilizing these bioportals. We selected three molecularly-driven clinical trials currently enrolling patients at Vanderbilt-Ingram Cancer Center and evaluated the incremental contribution of genomic and clinical data to refinement of cohort identification. Utilizing data from the enterprise data warehouse (EDW), we assessed the potentially eligible patient population after addition of gene-level, alteration-level, vital status (known to be deceased), and date of last contact data elements to the data extraction query. Results: Utilizing gene-level and diagnosis data elements only, 68 potentially eligible patients were identified for these trials from a total of 7,200 patients whose NGS data was added to the EDW between 2010 and 2016. Addition of alteration-level detail eliminated 29% of these patients. Of the 53 remaining patients, incorporating vital status resulted in paring the potentially eligible cohorts by an additional 42%. Conclusions: This study demonstrates the added value of querying structured clinical and molecular data stored in the EDW to improve prescreen workflow efficiency and decrease manual review requirements. [Table: see text]
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Affiliation(s)
| | | | - Neha Jain
- Vanderbilt University Ingram Cancer Center, Nashville, TN
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Levy MA, Micheel C, Jain N, Mittendorf KF. Assessment of actionability of cancer genomic testing panels based on a structured clinical trial knowledge base. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.6533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
6533 Background: Today’s oncologist is responsible for choosing appropriate cancer genomics tests to inform patient treatment from multiple available platforms, weighing cost, availability, sensitivity and specificity, and clinical actionability. Knowledge-driven clinical decision support tools can assist clinicians in choosing the panel that is most informative in a given clinical space. Methods: Using a queryable knowledgebase of >1800 active clinical trials containing structured eligibility criteria curations for diagnosis and genomic alterations, we compared two CLIA-regulated genomic panels for clinical actionability over the landscape of solid, breast, and lung cancer clinical trials. Results: The larger panel (73 genes) was more actionable than the smaller panel (62 genes) in the breast cancer (10x more trials returned) and solid tumor (2.7x more trials returned) clinical trial space, while the smaller panel returned 1.2x more trials in the lung cancer space (see table). Conclusions: This analysis demonstrates that patient diagnosis has a significant effect on the potential clinical actionability of a given genomic panel. Further, this analysis demonstrates the clinical utility of knowledge-driven clinical decision support tools for test selection, especially given the often-limited tumor sample available, cost of genomic panel testing, and continuously shifting trial landscape. [Table: see text]
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Affiliation(s)
| | | | - Neha Jain
- Vanderbilt University Ingram Cancer Center, Nashville, TN
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Takizawa Y, Binshtein E, Erwin AL, Pyburn TM, Mittendorf KF, Ohi MD. While the revolution will not be crystallized, biochemistry reigns supreme. Protein Sci 2016; 26:69-81. [PMID: 27673321 DOI: 10.1002/pro.3054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 12/14/2022]
Abstract
Single-particle cryo-electron microscopy (EM) is currently gaining attention for the ability to calculate structures that reach sub-5 Å resolutions; however, the technique is more than just an alternative approach to X-ray crystallography. Molecular machines work via dynamic conformational changes, making structural flexibility the hallmark of function. While the dynamic regions in molecules are essential, they are also the most challenging to structurally characterize. Single-particle EM has the distinct advantage of being able to directly visualize purified molecules without the formation of ordered arrays of molecules locked into identical conformations. Additionally, structures determined using single-particle EM can span resolution ranges from very low- to atomic-levels (>30-1.8 Å), sometimes even in the same structure. The ability to accommodate various resolutions gives single-particle EM the unique capacity to structurally characterize dynamic regions of biological molecules, thereby contributing essential structural information needed for the development of molecular models that explain function. Further, many important molecular machines are intrinsically dynamic and compositionally heterogeneous. Structures of these complexes may never reach sub-5 Å resolutions due to this flexibility required for function. Thus, the biochemical quality of the sample, as well as, the calculation and interpretation of low- to mid-resolution cryo-EM structures (30-8 Å) remains critical for generating insights into the architecture of many challenging biological samples that cannot be visualized using alternative techniques.
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Affiliation(s)
- Yoshimasa Takizawa
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Elad Binshtein
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Amanda L Erwin
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Tasia M Pyburn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
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Schlebach JP, Narayan M, Alford C, Mittendorf KF, Carter BD, Li J, Sanders CR. Conformational Stability and Pathogenic Misfolding of the Integral Membrane Protein PMP22. J Am Chem Soc 2015; 137:8758-68. [PMID: 26102530 PMCID: PMC4507940 DOI: 10.1021/jacs.5b03743] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Despite broad biochemical
relevance, our understanding of the physiochemical
reactions that limit the assembly and cellular trafficking of integral
membrane proteins remains superficial. In this work, we report the
first experimental assessment of the relationship between the conformational
stability of a eukaryotic membrane protein and the degree to which
it is retained by cellular quality control in the secretory pathway.
We quantitatively assessed both the conformational equilibrium and
cellular trafficking of 12 variants of the α-helical membrane
protein peripheral myelin protein 22 (PMP22), the intracellular misfolding
of which is known to cause peripheral neuropathies associated with
Charcot–Marie–Tooth disease (CMT). We show that the
extent to which these mutations influence the energetics of Zn(II)-mediated
PMP22 folding is proportional to the observed reduction in cellular
trafficking efficiency. Strikingly, quantitative analyses also reveal
that the reduction of motor nerve conduction velocities in affected
patients is proportional to the extent of the mutagenic destabilization.
This finding provides compelling evidence that the effects of these
mutations on the energetics of PMP22 folding lie at the heart of the
molecular basis of CMT. These findings highlight conformational stability
as a key factor governing membrane protein biogenesis and suggest
novel therapeutic strategies for CMT.
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Affiliation(s)
| | | | - Catherine Alford
- #Flow Cytometry Core, Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37232, United States
| | | | | | - Jun Li
- ⊥Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37232, United States
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Mittendorf KF, Kroncke BM, Meiler J, Sanders CR. The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing. Biochemistry 2014; 53:6139-41. [PMID: 25243937 PMCID: PMC4188248 DOI: 10.1021/bi500809t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Peripheral myelin protein 22 (PMP22)
is a tetraspan membrane protein
strongly expressed in myelinating Schwann cells of the peripheral
nervous system. Myriad missense mutations in PMP22 result in varying
degrees of peripheral neuropathy. We used Rosetta 3.5 to generate
a homology model of PMP22 based on the recently published crystal
structure of claudin-15. The model suggests that several mutations
known to result in neuropathy act by disrupting transmembrane helix
packing interactions. Our model also supports suggestions from previous
studies that the first transmembrane helix is not tightly associated
with the rest of the helical bundle.
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Affiliation(s)
- Kathleen F Mittendorf
- Department of Biochemistry, ‡Center for Structural Biology, and §Departments of Pharmacology and Bioinformatics, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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Song Y, Mittendorf KF, Lu Z, Sanders CR. Impact of bilayer lipid composition on the structure and topology of the transmembrane amyloid precursor C99 protein. J Am Chem Soc 2014; 136:4093-6. [PMID: 24564538 PMCID: PMC3985881 DOI: 10.1021/ja4114374] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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C99
(also known as β-CTF) is the 99 residue transmembrane
C-terminal domain (residues 672–770) of the amyloid precursor
protein and is the immediate precursor of the amyloid-β (Aβ)
polypeptides. To test the dependence of the C99 structure on the composition
of the host model membranes, NMR studies of C99 were conducted both
in anionic lyso-myristoylphosphatidylglycerol (LMPG) micelles and
in a series of five zwitterionic bicelle compositions involving phosphatidylcholine
and sphingomyelin in which the acyl chain lengths of these lipid components
varied from 14 to 24 carbons. Some of these mixtures are reported
for the first time in this work and should be of broad utility in
membrane protein research. The site-specific backbone 15N and 1H chemical shifts for C99 in LMPG and in all five
bicelle mixtures were seen to be remarkably similar, indicating little
dependence of the backbone structure of C99 on the composition of
the host model membrane. However, the length of the transmembrane
span was seen to vary in a manner that alters the positioning of the
γ-secretase cleavage sites with respect to the center of the
bilayer. This observation may contribute to the known dependency of
the Aβ42-to-Aβ40 production ratio on both membrane thickness
and the length of the C99 transmembrane domain.
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Affiliation(s)
- Yuanli Song
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-8725, United States
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Schlebach JP, Peng D, Kroncke BM, Mittendorf KF, Narayan M, Carter BD, Sanders CR. Reversible folding of human peripheral myelin protein 22, a tetraspan membrane protein. Biochemistry 2013; 52:3229-41. [PMID: 23639031 DOI: 10.1021/bi301635f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Misfolding of the α-helical membrane protein peripheral myelin protein 22 (PMP22) has been implicated in the pathogenesis of the common neurodegenerative disease known as Charcot-Marie-Tooth disease (CMTD) and also several other related peripheral neuropathies. Emerging evidence suggests that the propensity of PMP22 to misfold in the cell may be due to an intrinsic lack of conformational stability. Therefore, quantitative studies of the conformational equilibrium of PMP22 are needed to gain insight into the molecular basis of CMTD. In this work, we have investigated the folding and unfolding of wild type (WT) human PMP22 in mixed micelles. Both kinetic and thermodynamic measurements demonstrate that the denaturation of PMP22 by n-lauroyl sarcosine (LS) in dodecylphosphocholine (DPC) micelles is reversible. Assessment of the conformational equilibrium indicates that a significant fraction of unfolded PMP22 persists even in the absence of the denaturing detergent. However, we find the stability of PMP22 is increased by glycerol, which facilitates quantitation of thermodynamic parameters. To our knowledge, this work represents the first report of reversible unfolding of a eukaryotic multispan membrane protein. The results indicate that WT PMP22 possesses minimal conformational stability in micelles, which parallels its poor folding efficiency in the endoplasmic reticulum. Folding equilibrium measurements for PMP22 in micelles may provide an approach to assess the effects of cellular metabolites or potential therapeutic agents on its stability. Furthermore, these results pave the way for future investigation of the effects of pathogenic mutations on the conformational equilibrium of PMP22.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Biochemistry and ‡Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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Abstract
Alternative splicing (AS) of RNA is a key mechanism for diversification of the eukaryotic proteome. In this process, different mRNA transcripts can be produced through altered excision and/or inclusion of exons during processing of the pre-mRNA molecule. Since its discovery, AS has been shown to play roles in protein structure, function, and localization. Dysregulation of this process can result in disease phenotypes. Moreover, AS pathways are promising therapeutic targets for a number of diseases. Integral membrane proteins (MPs) represent a class of proteins that may be particularly amenable to regulation by alternative splicing because of the distinctive topological restraints associated with their folding, structure, trafficking, and function. Here, we review the impact of AS on MP form and function and the roles of AS in MP-related disorders such as Alzheimer's disease.
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Affiliation(s)
- Kathleen F Mittendorf
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Abstract
Membrane lipid composition can vary dramatically across the three domains of life and even within single organisms. Here we review evidence that the lipid-exposed surfaces of membrane proteins have generally evolved to maintain correct structure and function in the face of major changes in lipid composition. Such tolerance has allowed evolution to extensively remodel membrane lipid compositions during the emergence of new species without having to extensively remodel the associated membrane proteins. The tolerance of membrane proteins also permits single-cell organisms to vary their membrane lipid composition in response to their changing environments and allows dynamic and organelle-specific variations in the lipid compositions of eukaryotic cells. Membrane protein structural biology has greatly benefited from this seemingly intrinsic property of membrane proteins: the majority of structures determined to date have been characterized under model membrane conditions that little resemble those of native membranes. Nevertheless, with a few notable exceptions, most experimentally determined membrane protein structures appear, to a good approximation, to faithfully report on native structure.
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Affiliation(s)
- Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, USA.
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